Local cation-tuned reversible single-molecule switch in electric double layer

The nature of molecule-electrode interface is critical for the integration of atomically precise molecules as functional components into circuits. Herein, we demonstrate that the electric field localized metal cations in outer Helmholtz plane can modulate interfacial Au-carboxyl contacts, realizing a reversible single-molecule switch. STM break junction and I-V measurements show the electrochemical gating of aliphatic and aromatic carboxylic acids have a conductance ON/OFF behavior in electrolyte solution containing metal cations (i.e., Na+, K+, Mg2+ and Ca2+), compared to almost no change in conductance without metal cations. In situ Raman spectra reveal strong molecular carboxyl-metal cation coordination at the negatively charged electrode surface, hindering the formation of molecular junctions for electron tunnelling. This work validates the critical role of localized cations in the electric double layer to regulate electron transport at the single-molecule level.

This paper reports on the effect of local cations in the electric double layer on the formation of single molecule junctions (SMJs). The used molecules bear carboxylate groups which are affected by a) the potential applied to the substrate of the device, b) the used electrolyte. The subject is of interest for the readers of nature communication but in my opinion, the claim that a reversible single molecule switch is observed is strongly oversold and the highlighted On/Off ratio exceeding 104 is not correct. Because of these two reasons, I cannot recommend this paper for publication in nature communication. I agree that the authors show that molecules bearing terminal COOH groups do not bind to an STM tip in a similar way when the potential applied to the Au(111) substrates is varied. When it is higher than the potential of zero charge in NaClO4 solution, SMJs with conductance around 10-3 G0 can be generated. However, when the applied potential is lower than the potential of zero charge, the authors show that it is now impossible to fabricate an SMJ. Changing NaClO4 solution to NH4Cl or HCLO4 solutions makes it possible to generate SMs at various applied potential. This is an interesting observation that has interest for the researchers working in the field of SMJs and I agree that it reveals that the local metal cations in the Helmholtz plane can significantly affect Aucarboxyl contacts to form molecular junctions for electron transport. However, I also believe that no switching effects is really demonstrated in this paper. Indeed, to demonstrate a switch, it is in my opinion necessary to show I(V) curves (at constant bias) of the single molecule junctions and not only the fact that the applied potential to the substrate has an impact on the number of SMJ that can be obtained. V gate could be swept and during the sweep breaking of the SMJ could be observed. This is not what is reported in this manuscript. This is particularly true in the I-t curves presented in Figure 5 (d) in which no switch between On and Off states are observed. The red figure is measured with a applied potential of 0 V and a "stable" (8 seconds) SMJ is obtained while the green curve is measured with an applied potential of -0.5 V and No SMJ are seen during 8 seconds. Besides the way the I(t) curves are obtained with Au tip driven to approach until reaching a current value of 4 nA via piezo electric control with a bias voltage of 50 mV seems to be impossible to use when the gate voltage applied to the substrate is -0.5 V as in these conditions no SMJs are generated. In other words, the distance between the tip and the substrate for the green curve is difficult to control and if it is too high it is likely that the observed low current (at the limit of detection) is not significant of the claimed SMJ switch. This clearly question the reported On/OFF ratio above 104. Note also that such a apparent "switch", with a similar On/OFF ratio,, can be obtained by just retracting the tip in STM-BJ experiments which is what is observed in one of the red curves of figure 2b. Note also that I(Vgate) curves at fixed bias have been reported by several groups working with junctions using few electroactive molecules or few conjugated polymer wires and that switch behavior when changing the gate voltage was in these studies been demonstrated (see Tao or Lacroix work on Polyaniline for instance or Amatore or Mayor and Borguet work on small electoactive molecules) (I agree that ON/OFF ratios are small but switching behavior is clearly demonstrated) Overall, I believe that the results reported in this manuscript are interesting but that the way they are presented highlighting a switching behavior is misleading and that a reversible single molecule switch with On/Off ratio exceeding 104 is not demonstrated. There are also few technical issues to solve prior to publication in another journal. Indeed, the used reference electrode (Platinium?? ) is not an usual reference electrode in electrochemistry and its potential is likely to vary with the used solution (it just does not act as a reference). Moreover, from the experimental section it is not easy to see if the same platinum electrode acts as reference and counter electrode or if the used setup is using four electrodes (a Pt reference, a Pt counter, the Au(111) substrate) and the Au STM tip) This must be better explained. Finally, I am not so sure about the attribution of the electrochemical signal observed in Figure 3a mainly because the used reference is a Pt tip. It is attributed to deprotonation or protonation of the carboxyl groups, but this is NOT a redox reaction and carboxyl group are not electroactive (or is they are, at high potential, decarboxylation can occur) so deprotonation and protonation alone cannot be responsible of the observed current in figure 3a. This clearly need to be clarified using a more classical reference electrode prior to any publication.
Reviewer #3 (Remarks to the Author): The study by Tong, Yu, Gao et al reports single-molecule conductance measurements under electrochemical control. The conductance depends on both the potential of the electrode, and the presence of metal ions in solution, in a way that is exploited by the authors to demonstrate switching behaviour. The conclusions drawn from the conductance measurements are supported by Raman spectroscopy and control experiments. I find the study well carried out, interesting, and suitable for Nature Communications. There are some points, however, I would like to see clarified before publication. How are the molecules self-assembled on the Au surface? Are factors such as density and order important? I have some questions about the DFT part. Firstly, is it appropriate for the problem at hand? Without benchmarking the functional and basis set, modelling the second gold surface and the solvent environment, and accounting for effects such as basis set superposition error, how quantitative do the authors expect the calculated adsorption values to be? If the trend is only expected to be qualitative, then this should be stated. The authors state in the introduction that 'DFT simulations reveal strong molecular carboxyl-metal-cation coordination at the negatively charged electrode surface'. I'm not sure that the calculated adsorption energies show the strength of the carboxyl-metal cation coordination, but rather the effect of the additional presence of the gold cluster in the specific geometries presented. Does adding in NH4Cl or HClO4 (or indeed any of the salts) alter the pH of the solution, and in turn does this affect the conductance (e.g. Ref 33-J. Phys. Chem. Lett. 2020, 11, 23, 10023-10028)? The peak at -0.5 V for HClO4 is noticeably higher conductance that for the others. Could the authors add a table of conductances (including errors) to the supplementary information? The peak for the NH4Cl at 0 V is particularly weak. Are the authors sure there is a peak really there, and is the weakness also an effect of pH? It is surprising that the switching effect is reversible with Ca2+, previous reports have shown that binding leads to the loss of the reversible features in the CV, see e.g. Electrochimica Acta 53 (2008) 6759-6767. Could the authors comment on this? Why is the aliphatic MPA more conductive than the aromatic MTBA? Pi-conjugated molecules normally have closer levels for mediating transport. Is this just an effect of molecular length or the molecular structure affecting the pKa of the acid? ON/OFF ratio is just one part of a switch performance. How many cycles can be achieved? What are the limitations on frequency? Here are some minor comments. There are four typos in the second sentence of the abstract. E, written in Fig. 1b, should be defined in the caption or rewritten as Eads. Line 43. 'Wieldy' should read 'widely' Line 113. Full stop missing. Line 121. The authors state that 'Experimental details could be found in the Supplementary Information', however most are in the Methods section. In Fig 4 (and Fig 1.) The authors use <<PZC, ~PZC, >>PZC, these inequalities should have a value on either side (e.g. V << PZC). In Fig. 5d, put a y-axis label on at 0 nA so the magnitude of the current (not just the variation) can be seen. Line 272 'Quantitative statistics' seems a bit of an exaggeration of fitting to a Gaussian to a section of the I-t trace. Why just choose a section? I think at least add some error bars to value of 3.8 nA. Line 278. 'To conclusion' should read 'In conclusion' 2) It is interestingly found that the local concentrated metal cations in OHP can significantly affect the Au-COOcontacts at lower potentials than PZC, thereby hindering the formation of molecular junctions. In this case, the concentrations of metal cations in solution might also have an impact. I suggest the authors add potentialdependent single-molecule conductance measurements in another concentration of metal cations to confirm this interesting phenomenon.

Response:
We have supplemented the electrochemical gating of single-molecule conductance measurements in 0.1 mM 4-MTBA + 1 M Ca(ClO4)2 solution. The potential-dependent 1D conductance histogram of 4-MTBA in 1 M Ca(ClO4)2 are shown in Fig. R2. As the potential decreases, the conductance peak at 10 -3.0 G0 becomes weaker and disappears below -0.2 V in 1 M Ca(ClO4)2, which is 0.1 V earlier than in 0.05 M Ca(ClO4)2. This suggests that higher concentration of cations in the bulk solution leads to more concentrated metal cations in OHP affecting the Au-COOcontact. In response to reviewer's concerns, we have added a discussion "Increasing the electrolyte concentration can make the conductance peak disappear at higher potentials ( Supplementary Fig.11)" in the revised manuscript, and added 3) 4-MTBA has an asymmetric anchoring group. It has been reported that the asymmetric molecular structure has an effect on electron transport when changing the polarity of the bias voltage. Can these locally cation-tuned switches work when changing the polarity of the bias voltage?

Response:
The cation-tuned conductance switch remains effective when changing the polarity of the bias voltage. We have supplemented the single-conductance measurements in 50 mM NaClO4 solution with a fixed negative bias voltage of -50 mV (Esubstrate -Etip). As shown in Fig. R3, an obvious conductance peak at 10 -2.9 G0 can be observed at 0 V, while it disappears at -0.5 V, similar to that with a positive bias voltage of 50 mV in Fig. 2c. Therefore, the potential-controlled conductance switch can still work when changing the polarity of the bias voltage.

Response:
We have supplemented the CVs of Au (111) in 50 mM HClO4 solution. As shown in Fig. R4, there is one pair of well-defined reversible peaks at about 0.05 V. A linear correlation between current density of oxidation (red square) or reduction (blue square) with the scan rates is found. This proves that the reversible peaks arise from the 4-MTBA assembled on the Au(111) interface, which is similar to the 4-MTBA assembled on the Au(111) in 50 mM NaClO4 solution.

Response:
We thank the reviewer very much for the correction, and have carefully checked the manuscript and revised typo and format errors marked with yellow.

Reviewer: 2
Comments to the Author This paper reports on the effect of local cations in the electric double layer on the formation of single molecule junctions (SMJs). The used molecules bear carboxylate groups which are affected by a) the potential applied to the substrate of the device, b) the used electrolyte.
The subject is of interest for the readers of nature communication but in my opinion, the claim that a reversible single molecule switch is observed is strongly oversold and the highlighted On/Off ratio exceeding 10 4 is not correct. Because of these two reasons, I cannot recommend this paper for publication in nature communication.

Response:
We greatly appreciate the reviewer's constructive comments. To further prove the conductance On/Off ratio, we have supplemented the I-V (at a constant bias) tests. As shown in Fig. R5, obviously, the current jumps to a low value or a high value during a negative or positive potential sweep, respectively. These be attributed to the breakdown and formation of molecular junctions. The relative current difference is about 3.83 nA comparable to single-molecule conductance in the break junction measurements. When the gate potential is lower than −0.4 V, tip current is turned off for all I-V parallel tests (Fig. R5), which is consistent with the disappearance of conductance peak below −0.4 V in single-molecule break junction experiments. These further prove the local-cation controlled single-molecule switch.
In light of reviewer's constructive comments, we have changed the title to "Local cation-tuned reversible single-molecule switch in electric double layer" and removed the highlight of On/Off ratio exceeding 10 4 in the abstract. We have added  Fig.19), which is consistent with the disappearance of conductance peak below -0.4 V in single-molecule break junction experiments. These further prove the local-cation controlled single-molecule switch." in the revised in the manuscript.
I agree that the authors show that molecules bearing terminal COOH groups do not bind to an STM tip in a similar way when the potential applied to the Au(111) substrates is varied. When it is higher than the potential of zero charge in NaClO4 solution, SMJs with conductance around 10 -3 G0 can be generated. However, when the applied potential is lower than the potential of zero charge, the authors show that it is now impossible to fabricate an SMJ. Changing NaClO4 solution to NH4Cl or HClO4 solutions makes it possible to generate SMs at various applied potential. This is an interesting observation that has interest for the researchers working in the field of SMJs and I agree that it reveals that the local metal cations in the Helmholtz plane can significantly affect Au-carboxyl contacts to form molecular junctions for electron transport.

Response:
We greatly appreciate the reviewer for his/her positive comments on our work. 1) However, I also believe that no switching effects is really demonstrated in this paper. Indeed, to demonstrate a switch, it is in my opinion necessary to show I(V) curves (at constant bias) of the single molecule junctions and not only the fact that the applied potential to the substrate has an impact on the number of SMJ that can be obtained. V gate could be swept and during the sweep breaking of the SMJ could be observed. This is not what is reported in this manuscript. This is particularly true in the I-t curves presented in Figure 5 (d) in which no switch between On and Off states are observed. The red figure is measured with an applied potential of 0 V and a "stable" (8 seconds) SMJ is obtained while the green curve is measured with an applied potential of -0.5 V and No SMJ are seen during 8 seconds. Besides the way the I(t) curves are obtained with Au tip driven to approach until reaching a current value of 4 nA via piezo electric control with a bias voltage of 50 mV seems to be impossible to use when the gate voltage applied to the substrate is -0.5 V as in these conditions no SMJs are generated. In other words, the distance between the tip and the substrate for the green curve is difficult to control and if it is too high it is likely that the observed low current (at the limit of detection) is not significant of the claimed SMJ switch. This clearly question the reported On/OFF ratio above 10 4 .

Response:
To further test the switching effects, we have supplemented the I-V measurements with a constant bias of 50 mV in 0.1 mM 4-MTBA + 50 mM NaClO4 solution. The procedure of I-V measurements is described as follows: First, the STM tip is driven toward the substrate to a preset current value (50 nA) via piezoelectric control. Then an external pulse voltage is applied on z-piezo to bring STM tip 1 nm into the substrate surface to ensure tip contact with the substrate. Next, the tip is withdrawn until the tip current value reaches single molecule conductance value (Equal to the molecular conductance 10 -3.0 G0 of 4-MTBA multiplied by 50 mV bias). When the single-molecule conductance is detected, the tip will be fixed over the substrate, and the substrate potential is swept between 0 to -0.5 V. Fig. R5a the traces of I-V curves recorded upon formation of molecular junctions. Obviously, the current jumps to a low value or a high value during a negative or positive potential sweep, respectively. These can be attributed to the breakdown and formation of molecular junctions. The relative current difference is about 3.83 nA comparable to single-molecule conductance in the break junction measurements. When the gate potential is lower than -0.41 V, tip current is turned off for all I-V parallel tests (Fig. R5b), which is consistent with the disappearance of conductance peak below −0.4 V in single-molecule break junction experiments. These further prove the local-cation controlled single-molecule switch.
For I-t measurements, we apologize for the wrong description of the experimental details. We agree that the tip-to-substrate distance is difficult to know in STM-BJ experiments. Certainly, when tip-to-substrate distance is larger than the molecular length, molecular junction will not form to observe the current spikes in the I-t curves.
However, in the constant current mode of STM, the distance from the tip to the substrate can be controlled by the preset current value. In our experiments, we optimized the current setpoint values to 4 nA at the substrate potential of 0 V, at which the molecular junction can be formed based on the break junction measurements. We recorded the It curves with a very low feedback loop of 0.01 at the substrate potentials of 0 and -0.5 V, respectively. It was found that the current spikes ascribed to form molecular junctions disappeared at -0.5 V, which verified this local-cation control switch consistent with the results of break junction measurements. Note also that such an apparent "switch", with a similar On/OFF ratio, can be obtained by just retracting the tip in STM-BJ experiments which is what is observed in one of the red curves of figure 2b.

Response:
We agree that molecular junctions would be broken by withdrawing the tip away from the substrate beyond the molecular length, which can cause a rapid decrease in conductance for all kinds of molecular junctions. Such mechanical control has also been used to realize conductance switching in a single-molecule junction (Nat. Nanotech., 2009, 4, 230-234;Nat. Nanotech. 2012, 7,35-40;Angew. Chem. Int. Ed.,2023, doi: 10.1002. In our work, we found that the electrified localized metal cations in outer Helmholtz plane can strongly coordinate with molecular carboxyl-groups at the negatively charged electrode surface, which hinders the formation of molecular junctions for electron transport. Consequently, the step features in the conductance traces disappear at -0.5 V. This can also realize single-molecule conductance switch by potential control in our work instead of retracting the tip.
Note also that I(Vgate) curves at fixed bias have been reported by several groups working with junctions using few electroactive molecules or few conjugated polymer wires and that switch behavior when changing the gate voltage was in these studies been demonstrated (see Tao  Overall, I believe that the results reported in this manuscript are interesting but that the way they are presented highlighting a switching behavior is misleading and that a reversible single molecule switch with On/Off ratio exceeding 10 4 is not demonstrated.

Response:
We greatly appreciate the reviewer for his/her constructive comments, and we have further proven such switching behavior using I-V tests, and have changed the title to "Local cation-tuned reversible single-molecule switch in electric double layer" and removed the highlight of On/Off ratio exceeding 10 4 in the revised Abstract.
2) There are also few technical issues to solve prior to publication in another journal.
Indeed, the used reference electrode (Platinium?? ) is not an usual reference electrode in electrochemistry and its potential is likely to vary with the used solution (it just does not act as a reference). Moreover, from the experimental section it is not easy to see if the same platinum electrode acts as reference and counter electrode or if the used setup is using four electrodes (a Pt reference, a Pt counter, the Au(111) substrate and the Au STM tip) This must be better explained. Finally, I am not so sure about the attribution of the electrochemical signal observed in Figure 3a mainly because the used reference is a Pt tip. It is attributed to deprotonation or protonation of the carboxyl groups, but this is NOT a redox reaction and carboxyl group are not electroactive (or is they are, at high potential, decarboxylation can occur) so deprotonation and protonation alone cannot be responsible of the observed current in figure 3a. This clearly need to be clarified using a more classical reference electrode prior to any publication.
Response: In our STM-BJ setup, a four-electrode electrochemical system was used, the same Pt ring and Pt wire were used as counter electrode and reference electrode in the different experiments, respectively. There are two main reasons for using Pt as a quasireference electrode in our experiments. One is that the home-made cell (about 200 μL) for electrochemical STM experiments is too small to put in the commercial reference electrode. So most electrochemical STM experiments use metal wires as quasireference electrodes including Pt (Nat. Catal. 2021, 4, 850-859;Nat. Mater. 2019, 18, 357-363;J. Am. Chem. Soc. 2022, 144, 20126−20133). The other is the presence of chloride ions in the commercial reference electrodes of SCE and Ag/AgCl. Halogen ions can specifically adsorb and even etch the Au surface, especially at high potentials > PZC.
We have also supplemented the CVs of Au(111) in 0.1 mM 4-MTBA +50 mM NaClO4 solution with different scan rates using SCE as the reference electrode. As shown in Fig. R6, there is one pair of well-defined reversible peaks at about 0.4 V vs.
SCE. Plotting current density of oxidation (red square) or reduction (blue circle) with the scan rate, a linear correlation is also observed. The total charges of oxidation peaks are quantitatively estimated at about 14.5 µC/cm 2 consistent with the results using Pt as quasi-reference electrode in Fig. 3a. Such reversible peaks have also been observed at self-assembled monolayers of carboxylic acid molecules in previous reports (Langmuir, 2006, 22, 4420-4428;Electrochim. Acta,2008, 53, 6759-6767), which are assigned to deprotonation or protonation of the carboxyl groups in positive or negative scans of the electrochemical potentials. The degree of order of the molecular assembly layer should might have no effect on the formation of molecular connections. Fig. R7a shows the STM images of Au (111) in the 0.1 mM 4-MTBA aqueous solution. No ordered structure of the SAM of 4-MTBA was found under our experimental conditions. According to the previous report (Angew. Chem. Int. Ed. 2019, 58, 14534 -14538), the formation probability of methyl sulfide-linked molecular junction as a function of molecular concentration from 1×10 -7 to 5×10 -5 M fits well with the Langmuir isotherm. Continuing to increase the concentration of molecules, the intensity of the conductance peak hardly changes due to molecular adsorption saturation. Thus, the molecular concentration of 0.1 mM (1×10 -4 M) can ensure that there is enough molecular adsorption to maximize the probability of junction formation.  In order to approach the experimental environments, another three-layer 2×2 Au(111) surface with thinner vacuum layer was constructed to simulate the presence of gold electrodes at both terminals. The results showed that the thickness of the vacuum layer also has barely effect on the trend of adsorption energy for this system.  (111) and aqueous phase/Au(111) system.    According to reviewer's suggestion, we have replaced Fig. 1b with Fig. R10, and revised the discussion to "To substantiate this hypothesis, we firstly performed density function theory (DFT) Fig. 1 and 2 in Supplementary Information). Fig.1b- . According to previous report (J. Phys. Chem. Lett.,2020,11, 23, 10023-10028), the conductance peak intensity in HClO4 should be the weakest. However, our experiments found the opposite.

and ab initio molecular dynamics (AIMD) calculations to analyse the interaction between carboxylic acid molecules and Au electrode in different configurations using the Vienna Ab Initio Simulation Package (VASP) software (see Methods and Supplementary
Combining Raman spectroscopy and theoretical calculations, we prove that strong molecular carboxyl-metal-cation coordination at the negatively charged electrode surface hinders the formation of molecular junctions.  Table R1 in the revised supplementary information. 4) The peak for the NH4Cl at 0 V is particularly weak. Are the authors sure there is a peak there, and is the weakness also an effect of pH?

Response:
We have shown its 1D and 2D conductance histograms in Fig. R11a and b, it can be found a conductance peak and an obvious stretching states centered around 10 -3.0 G0. There may be two main reasons for the weaker conductance peak intensity in   Response: We agree with that the π-conjugated molecules generally exhibit larger conductance values with smaller HOMO-LUMO gaps for electron transport. While the molecular length is another important factor determining the single-molecule conductance. Our previous report found that the pH of solution or the pKa of carboxylic acid molecule affects the probability of molecular junction formation, but has little impact on its conductance value (J. Phys. Chem. Lett. 2020, 11, 10023−10028). Thus, we think that the aliphatic MPA is more conductive than aromatic MTBA due to its shorter molecular length.
We have supplemented the cyclic tests by repeatedly cyclically sweeping the potential between 0 and -0.

Response:
We have corrected the sentence to "Experimental details could be found in Method section".
In Fig 4 (and Fig 1.) The authors use <>PZC, these inequalities should have a value on either side (e.g. V << PZC).
In Fig. 5d, put a y-axis label on at 0 nA so the magnitude of the current (not just the variation) can be seen.

Response:
We have marked 0 nA for the y-axis in the revised Fig. 5d.
Line 272 'Quantitative statistics' seems a bit of an exaggeration of fitting to a Gaussian to a section of the I-t trace. Why just choose a section? I think at least add some error bars to value of 3.8 nA.

Response:
We apologize for our imprecise, and have corrected the current value to 3.68±0.55 nA based on Gaussian fit in the entire I-t trace.

Reviewer #1 (Remarks to the Author):
The authors addressed the questions raised by the reviewers and I suggest to accept it as it is.
Reviewer #2 (Remarks to the Author): I read carefully the revised version of the manuscript now entitled « local Cation tuned reversible single-molecule switch in electric double layer. It is much more convincing and its subject is clearly of interest for the readers of Nature communication.

Many of my initial comments have been taken into account. The title has been changed and is now more in line with the findings and the I/V characterization in figure 5f now clearly show a switch between On and Off state. I thus recommend publication in nature communication. However, there is still some important modifications to address prior to publish the paper. The three following points must be changed. a) CV of figure 3a show a peak which is attributed to deprotonation/protonation of the carboxyl groups with the help of two references given (ref40 et 41). The author MUST add that there is no faradic processes taking place within this electrochemical potential range. This fact is clearly stated in Reference 41 and even though it is true that in 2008 a similar peak as the one shown here was reported (in reference 40) it remains important to say that this is not linked to any faradic processes. (deprotonation/protonation are not redox events) From reference 41 this is clearly stated the P1 peak is not attributed to protonation/deprotonation but to a reorganization of the ad layers on the surface. b) I still have problem with the claimed ON/OFF ratio of conductance (or current) Indeed
, the paper clearly demonstrate that there is a preferred conductance peak in some electrolyte when the applied potential is positive and that there is no conductance peak (i.e ; no single molecule junction) when the potential is below -0.3V (see figure 3b for instance) but this does not mean that the ON/OFF ratio exceeds 6.7 104 as claimed. Indeed, if we concentrate on the value of the measured current when no SMJs are obtained (at -0.5V), in figure 3b, there is current counts at all current values including for currents higher than that observed for the peak at 0.1 V. So the ratio of current is not 6.7 104 and can in fact be anything. If one now looks at the curves given in figure 5f, the current ON is around 4 nA and the current OFF is below 1 nA but is not at all 6.7 104 smaller than the current ON. Current Off is not small because there is leakage and in fact no SMJ are created but the tip is still not far away to the surface and if there is a little bit feedback loop as stated in the caption then the tip will try to move and get closer to the surface and reach the current set point used. In my opinion it is impossible to state that the ON/OFF ratio exceeds for order of magnitude as stated in Overall the paper is interesting with a very nice new concept but On/off ratio above 10 power 4 remains in my opinion not clearly demonstrated in the presented data.

Reviewer #3 (Remarks to the Author):
The study is improved by enacting the changes. I still find think it is suitable for Nature Communications, as the science is sound and the results are convincing and well-supported by the data, but some issues need to be clarified. Regarding the switch performance I'm a little confused by Fig. 5. Is it correct that the conductance values in Fig. 5a -5c are taken from fitting to conductance of many junctions followed by averaging? This should be clarified. In Fig. 5d the I(t) trace at -0.5 V has a mean value of ~ 4nA , so if translated into a Gaussian as done for the trace at 0 V in Fig. 5e it will appear at the same mean value but narrower, as there are no spikes present. I'm not sure what this adds to the switching behaviour, in my mind these I(t) traces at a fixed bias imply the device could act as a sensor rather than a switch, -it reminds me of e.g. https://www.nature.com/articles/ncomms13868. Additionally, regarding the issue of reporting the ON/OFF ratio as 6.7x104 -I find removing it from just the abstract a strange course of action. Either it is correct, and can remain wherever, or it is incorrect/dubious, and then should be removed or heavily caveated. Overall, some re-writing or restructuring of the discussion around Fig. 5 should be undertaken to clarify these, discussing limitations, and possibly other potential uses. Finally, there are still typos remaining, including some that I explicitly mentioned in my first review, that I won't repeat here. Units are missing from Fig 5e.

Replies to Reviewers
Reviewer #1: The authors addressed the questions raised by the reviewers and I suggest to accept it as it is.

Response:
We greatly appreciate the reviewer for his/her valuable time and constructive comments in improving the quality of this manuscript.

Reviewer #2:
I read carefully the revised version of the manuscript now entitled « local Cation tuned reversible single-molecule switch in electric double layer. It is much more convincing and its subject is clearly of interest for the readers of Nature communication.

Response:
We greatly appreciate the reviewer for his/her positive and constructive comments of our work.
Many of my initial comments have been taken into account. The title has been changed and is now more in line with the findings and the I/V characterization in figure 5f now clearly show a switch between On and Off state. I thus recommend publication in nature communication. However, there is still some important modifications to address prior to publish the paper.
The three following points must be changed.
a) CV of figure 3a show a peak which is attributed to deprotonation/protonation of the carboxyl groups with the help of two references given (ref40 et 41). The author MUST add that there is no faradic processes taking place within this electrochemical potential range. This fact is clearly stated in Reference 41 and even though it is true that in 2008 a similar peak as the one shown here was reported (in reference 40) it remains important to say that this is not linked to any faradic processes. (deprotonation/protonation are not redox events) From reference 41 this is clearly stated the P1 peak is not attributed to protonation/deprotonation but to a reorganization of the ad layers on the surface.

Response:
We thank the reviewer very much for the correction, we have revised the "A linear correlation between current density of oxidation (red square) or reduction (blue square)" to "A linear correlation between anodic (red square) and cathodic (blue square) current peaks", "total charges of oxidation peaks" to the "total charges of anodic current peaks". We have also added a description "Due to the good stability of carboxylic acids, no faradaic processes occur in this electrochemical potential range." Indeed, the paper clearly demonstrate that there is a preferred conductance peak in some electrolyte when the applied potential is positive and that there is no conductance peak (i.e ; no single molecule junction) when the potential is below -0.3 V (see figure 3b for instance) but this does not mean that the ON/OFF ratio exceeds 6.7×10 4 as claimed.
Indeed, if we concentrate on the value of the measured current when no SMJs are obtained (at -0.5V), in figure 3b, there is current counts at all current values including for currents higher than that observed for the peak at 0.1 V. So the ratio of current is not 6.7×10 4 and can in fact be anything. If one now looks at the curves given in figure 5f, the current ON is around 4 nA and the current OFF is below 1 nA but is not at all 6.7×10 4 smaller than the current ON. Current Off is not small because there is leakage and in fact no SMJ are created but the tip is still not far away to the surface and if there is a little bit feedback loop as stated in the caption then the tip will try to move and get closer to the surface and reach the current set point used. In my opinion it is impossible to state that the ON/OFF ratio exceeds four order of magnitude as stated in Figure 5 Response: The point is: when no conductance peak is detected in STM-BJ experiments, can it be said that the conductance value is below the detection limit of the current amplifier? There are two situations in the current study that lead to the disappearance of the conductance peak: One is that the conductance of molecular junction is too small to be detected by current amplifiers in use; Another is that no molecular junction is There are current counts at all current values at -0.5 V in figure 3b, including some currents higher than that observed for the peak at 0 V, because the STM-BJ firstly forms metal atomic contacts, then the metal atomic contacts break, and form a nanogap that can trap molecules to form molecular junctions. If molecular junctions are not formed, there will also be an exponentially decaying tunneling current, including some current values higher than the conductance of single-molecule junctions.
We agree that the base current including tip leakage, Faraday and non-Faraday current can affect the current minimum and thus the switching ratio. The I-V traces in Fig. 5f is recorded with STM feedback loop turned off. It is worth pointing out that the I-V traces in Fig. 5f is a dynamic process by simultaneously scanning the potentials of Au tip and substrate. There is an additional charging current of electric double layer to increase the base current, compared with STM-BJ experiments that performed at a specific potential in quasi-steady state. Thus, the tip current at the OFF state in Fig. 5f is larger.
According to the reviewer's constructive comments, we have removed the statement that ON/OFF ratio exceeds 6.7×10 4 in the revised manuscript, and added a description

Response:
The I(t) test with feedback loop at a fix bias can keep the relative distance between the tip and substrate by a preset current point. As the molecules are trapped into the nanogap between the two electrodes to form molecular junctions, the characteristic electron tunnel-current spikes can be observed on the I-t curves, which have been used to electronic single-molecule identification and sensors (Nat. Nanotechnol., 2010, 5, 868-873;Nat Commun.,2016, 7, 13868). This has also been pointed out by Reviewer #3. Thus, we performed I(t) tests with feedback loop at 0 and -0.5 V in Figure 5d (now is Supplementary Fig. 19a) to proves the molecules can be trapped and tethered to two electrodes to form molecular junction at positively charged electrode surface, rather than at negatively charged electrode surface. Fig. 5e (now is Supplementary Fig. 19b) is the statistics of relative height of current spikes in the I-t curves with shifting the baseline of tunnelling current (4 nA) to zero. As Reviewer #3 said, these current spikes in I-t traces could act as a sensor rather than a switch. We have corrected this part in the revised manuscript.   Fig. 19). These further confirm that the electric field localized cations at different charged electrode surface can modulate the molecule-metal contacts, leading to conductance ON/OFF states." in the revised manuscript.
Overall the paper is interesting with a very nice new concept but ON/OFF ratio above 10 power 4 remains in my opinion not clearly demonstrated in the presented data.

Response:
We greatly appreciate the reviewer for his/her valuable time and constructive comments in improving the quality of this manuscript. We have removed the statement that ON/OFF ratio exceeds 6.7×10 4 in the revised manuscript.

Reviewer #3:
The study is improved by enacting the changes. I still find think it is suitable for Nature Communications, as the science is sound and the results are convincing and wellsupported by the data, but some issues need to be clarified.

Response:
We greatly appreciate the reviewer for his/her positive comments of our work.
Regarding the switch performance I'm a little confused by Fig. 5. Is it correct that the conductance values in Fig. 5a -5c are taken from fitting to conductance of many junctions followed by averaging? This should be clarified.
Response: Yes, the conductance values in Fig. 5a  In Fig. 5d the I(t) trace at -0.5 V has a mean value of ~ 4nA , so if translated into a Gaussian as done for the trace at 0 V in Fig. 5e it will appear at the same mean value but narrower, as there are no spikes present. I'm not sure what this adds to the switching behaviour, in my mind these I(t) traces at a fixed bias imply the device could act as a sensor rather than a switch, -it reminds me of e.g. https://www.nature.com/articles/ncomms13868.

Response:
For the statistics of relative height of current spikes in the I-t curves, we have shifted the baseline of tunnelling current (4 nA) to zero. We agree that these current spikes in I-t traces in Fig. 5d (now is Supplementary Fig. 19a) could act as a sensor rather than a switch. We have also supplemented the I(t) test without feedback loop ( Fig. R1) according to the previous report (Nano Lett., 2021, 21, 6540-6548). At 0 V, current blinking can be observed at around t=10 s, then the current jumps to ON state for lasting more than 1 s, consistent with the previous report (Nano Lett., 2021, 21, 6540-6548). This similar phenomenon repeats around t=19 s. The current jump height is about 3.78 nA, corresponding to a conductance of 10 -3.0 G0, which is coherent with single-molecule conductance in the STM-BJ measurements. Instead, only the base current and its fluctuations were observed when the substrate potential was controlled at −0.5 V, indicating no molecular junction formation. These further confirm that the electric field localized cations at different charged electrode surface can modulate the molecule-metal contacts, leading to conductance ON/OFF states.
According to review's suggestion, we have cited the reference of Nat. Commun., 2016, 7, 13868, replaced the Fig. 5d with Fig. R1  Instead, only the base current and its fluctuations were observed when the substrate potential was controlled at −0.5 V. In addition, the I-t tests with a very low STM feedback loop [49][50][51] have also shown that the characteristic electron tunnel-current spikes ascribed to trapped molecules in the nanogap of two electrodes to form molecular junction at positively charged electrode surface, rather than at negatively charged electrode surface (Supplementary Fig.19). These further confirm that the electric field localized cations at different charged electrode surface can modulate the molecule-metal contacts, leading to conductance ON/OFF states." in the revised manuscript.
Additionally, regarding the issue of reporting the ON/OFF ratio as 6.7×10 4 -I find removing it from just the abstract a strange course of action. Either it is correct, and can remain wherever, or it is incorrect/dubious, and then should be removed or heavily caveated.
Response: Just like our response to Reviewer 2's question "b)", we have removed the description of the ON/OFF ratio of 6.7×10 4 in order to avoid this controversy.
The point is: when no conductance peak is detected in STM-BJ experiments, can it be said that the conductance value is below the detection limit of the current amplifier?
There are two situations in the current study that lead to the disappearance of the conductance peak: One is that the conductance of molecular junction is too small to be detected by current amplifiers in use; Another is that no molecular junction is formed.
In our experiments, there is no step feature in the conductance-displacement after rupturing Au atomic contacts in conductance-displacement traces at -0.5 V. With the help of Raman spectroscopy and theoretical simulations, we reveal that the strong molecular carboxyl-metal cation coordination at the negatively charged electrode surface hinders the formation of molecular junctions for electron tunnelling. To avoid controversy, we have removed the description of the ON/OFF ratio exceeds 6.7×10 4 in the revised manuscript, and added a description "The conductance peak disappears due to the strong molecular carboxyl-metal cation coordination on the negatively charged electrode surface, which is considered as the conductance off state. Thus, the conductance ON/OFF states might be effectively achieved through the electrochemical control." in the revised manuscript.
Overall, some re-writing or restructuring of the discussion around Fig. 5 should be undertaken to clarify these, discussing limitations, and possibly other potential uses.

Response:
We have changed Fig. 5 and rewritten the discussion, and we have also added a discussion to clarify the limits of the local-cation controlled single-molecule switch "In addition, it is worth mentioning that this local cation-tuned single-molecule switch depends on the rate at which the applied potential changes the structure of electric double layer. This might lead to low switching frequency. On the other hand, when the gate potential is changed, the base current including the electric double layer charging current and the tip leakage current can affect the switching performance such as ON/OFF ratio." in the revised manuscript.
Finally, there are still typos remaining, including some that I explicitly mentioned in